title: Virtual Screening for Dipeptide Aggregation: Toward Predictive Tools for Peptide Self-Assembly.
abstract: Several short peptide sequences are known to self-assemble into supramolecular nanostructures with interesting properties. In this study, coarse-grained molecular dynamics is employed to rapidly screen all 400 dipeptide combinations and predict their ability to aggregate as a potential precursor to their self-assembly. The simulation protocol and scoring method proposed allows a rapid determination of whether a given peptide sequence is likely to aggregate (an indicator for the ability to self-assemble) under aqueous conditions. Systems that show strong aggregation tendencies in the initial screening are selected for longer simulations, which result in good agreement with the known self-assembly or aggregation of dipeptides reported in the literature. Our extended simulations of the diphenylalanine system show that the coarse-grain model is able to reproduce salient features of nanoscale systems and provide insight into the self-assembly process for this system.
authors.affiliation: WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde , 295 Cathedral Street, Glasgow, G1 1XL, United Kingdom ; SUPA, Department of Physics, University of Strathclyde , 107 Rottenrow East, Glasgow, G4 0NG, United Kingdom.
authors.forename: Pim W J M
authors.initials: PW
authors.lastname: Frederix
authors.forename: Rein V
authors.initials: RV
authors.lastname: Ulijn
authors.forename: Neil T
authors.initials: NT
authors.lastname: Hunt
authors.forename: Tell
authors.initials: T
authors.lastname: Tuttle